FLRT3 p.Gln299=
c.897A>G · VCV3718439
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0187%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.66 | GERP -1.7, phastCons 1 |
| Overall | ||
| CADD | 6.233 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0187%
African / African-American · 14/75,006 alleles
Filtering AF
0.0112%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00903%
Overall
0.00136%
22/1,613,840 alleles · ultra-rare
exomes 12/1,461,598 · genomes 10/152,242 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0187% | 5,358 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,621 |
| Admixed American | 0.005% | 19,992 |
| European (non-Finnish) | 8.48e-05% | 1,179,834 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- FLRT3
- Protein
- p.Gln299=
- Coding
- c.897A>G
- MANE Select
- NM_198391
- Type
- single nucleotide variant
- Location
- chr20:14326610 (GRCh38)
- Gene constraint
- LOEUF 0.585 · pLI 0.55 (gnomAD)
- Structure
- AlphaFold pLDDT 74.57 · 3 PDB
- Residue 299
- a β-strand
Similar variants
- FLRT3 p.Arg163Cys Uncertain significance ★★ ⚠ same type
- FLRT3 p.Leu109Val Uncertain significance ★★ ⚠ same type
- FLRT3 p.Ser25Pro Uncertain significance ★★ ⚠ same type
- FLRT3 p.Ser284Arg Uncertain significance ★★ ⚠ same type
- FLRT3 p.Ser33Pro Uncertain significance ★★ ⚠ same type
- FLRT3 p.Thr199Ser Uncertain significance ★★ ⚠ same type
- FLRT3 p.Thr419Ser Uncertain significance ★★ ⚠ same type
- FLRT3 p.Trp381Arg Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/flrt3-p-gln299 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown